Clustering of protein linkers drives a dynamical arrest in condensates

Liquid–Liquid Phase Separation (LLPS) is a ubiquitous cellular mechanism that organizes proteins into dynamic, membraneless compartments. Over time, these condensates can undergo aging, transitioning from fluid, reversible assemblies to more rigid, less mobile structures. Condensate aging is implicated in neurodegeneration, but its underlying mechanism remains poorly understood. To address this, we utilize a model system of two non-interacting polymer species that can be crosslinked by bivalent linkers. Upon gradual annealing, polymer–linker contacts reorganize into fewer, denser clusters. The linkers form emergent “ladder” structures bridging the two polymer types, such that individual bond breakage is insufficient to allow polymer diffusion. Meanwhile, polymer segments flanking the ladder of linkers become unlinked, gaining greater conformational entropy. This system provides a minimal physical framework to investigate how specific linker–polymer interactions may influence condensate dynamics and potentially contribute to aging-like behavior.

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